This document walks through the Reorienting to Recovery’s Recovery Definition and evaluates how the Dry Years Blended Scenario Performs. It provides summary statistics and visualizations to evaluate recovery according to defined thresholds recovery metrics (Threshold Recovery Metrics table below) and to explore results associated with non thereshold biological metrics (Additional Biological Metrics table below).

Review Indicator Populations

The Reorienting to Recovery selected a few indicator populations as a starting point for evaluating recovery of scenarios. For the Fall Run Chinook model, we selected:

Indicator rivers must meet all recovery metrics in last 15 years of the simulation.

Secondarily, all independent populations must meet recovery in at least 5 years and the percentage of ind populations that meet recovery objects must be above 80% in last 15 years.

Review Biological Recovery Metrics

Threshold Recovery Metrics

The table below summarizes Recovery Metrics that have associated Recovery Thresholds. For each of these metrics, scenarios are evaluated to see what percentage or tributaries or years they achieve the recovery target for each scenario.

Value Performancemeasure Description Target/Recovery Threshold
1: Salmonid abundance 1: Adult abundance Represents an interest in increasing salmonid abundance across the Central Valley. Can be estimated with models as annual number of adult spawning salmonids in each tributary and ocean, tracked for 20 years. Adult abundance for each year and tributary is a direct output from the SIT DSMs and is summarized to show average Central Valley annual abundance. 500 or more spawners
2: Salmonid productivity 2.1: Cohort Replacement Represents an interest in having growing or stable salmonid populations. CRR can be estimated with models as the adult natural origin return ratio in each tributary, tracked for 20 years. CRR is calculated as the number of natural origin adult returns in year X+3 divided by the number of in-river spawners in year X. CRR is calculated for each year and tributary and then averaged across tributaries and years. Mean CRR > 1
2: Salmonid productivity 2.2: Population growth rate Represents an alternative way to capture growing or stable salmonid populations. Can be estimated with models as average trend in population growth over a 20-year period. Mean Growth Rate > 1
4: Salmonid genetic diversity 4: pHOS Represents an interest in preserving genetic diversity of natural populations and minimizing potential negative demographic effects from hatchery origin fish. Salmonid models are currently being modified to estimate proportion of hatchery origin spawners (pHOS). pHOS < 5%

Additional Biological Recovery Metrics

The table below provides additional recovery metrics to help balance and refine scenarios. This set of metrics does not have clear threshold values that indicate recovery but instead provides additional context to help select more balanced scenarios.

Value Performance measure Description
3: Salmonid spatial structure 3.1: Independent populations Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific abundance estimates from models can be used to calculate the number of independent viable populations in each diversity group per ESU/run.
3: Salmonid spatial structure 3.2: % of potential independent populations Represents an alternative way to capture the distribution of salmonid, calculated as the % of potential independent viable populations in each diversity group per ESU/run.
3: Salmonid spatial structure 3.3: Dependent populations Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific CV Salmon Recovery abundance estimates from models can be used to calculate the number of dependent populations in each diversity group per ESU/run.
5: Salmonid life history diversity 5.1: Age distribution of spawning adults Represents an interest in preserving life history diversity (age of spawners) in natural populations. Salmonid models can be used to estimate the minimum % of each age class of adults and check if targets are met (Age 4 >35%, Age 5+ >20%).
5: Salmonid life history diversity 5.2: Size distribution of juveniles Represents an interest in preserving life history diversity (size distribution of juveniles) in natural populations. Salmonid models can be used to estimate the variation in juvenile abundance of each life stage (fry, parr, yearling) and calculate variation across years. Size distribution of juveniles is summarized in a single metric by using a Shannon diversity index.
5: Salmonid life history diversity 5.3: Size and timing of juveniles at ocean entry Represents an interest in preserving life history diversity (size and timing of juveniles at ocean entry) in natural populations. Size distribution and timing of juveniles at ocean entry is summarized in a single metric by using a Shannon diversity index.
5: Salmonid life history diversity 5.4: Habitat diversity Represents an interest in preserving habitat diversity that facilitates life history diversity in natural populations. Could be estimated as the amount and relative % of available habitat of different types (measured in area and days). Specific methods using the salmon models to calculate and compare optimal habitat ratios to population growth are being developed.
6: Abundance, productivity, and distribution at levels that support ecosystem health 6: Ecosystem health Represents an interest in maintaining resilient and functioning ecosystems due to adequate salmonid abundance. Could be captured with a proxy metric of ratio of spawner abundance to habitat (marine derived nutrient proxy). The marine derived nutrient proxy metric gives the grams of marine nutrient per square meters of river. To calculate marine derived nutrient proxy, we calculated the total acres by multiplying habitat extent lengths by river width. We then multiplied the average annual number of spawners by the average weight (assumed 21 grams) and divided by our total area CV Salmon Recovery Draft for Planning Team Review 11 (square meters) to get a grams of marine derived nutrient per square meters.
7: Biological recovery objectives met by certain time 7: Time to biological recovery Represents an interest to recover salmonids quickly. Can be estimated by salmon models as the # of years until recovery objectives are met. See Phase 1 report for a list of recovery objectives.

Review Dry Years Scenario

The Dry Years scenario includes efforts in each of the 4 knobs that we can turn in the R2R process: Habitat, Hydrology, Harvest (oceans & rivers) and Hatcheries. The table below summarizes the Dry Years scenario in comparison to the Baseline scenario.

Recovery scenario Habitat Hydrology Harvest (oceans & rivers) Hatcheries
Baseline Current + planned Current operations Current levels Current operations
Dry Years Max habitat, Food subsidies, Predation reduction (Dry Years) EFF (dry years) No harvest of dry Cohort Terminal Hatcheries (current output number)

Run Dry Years Scenario

The following code block runs the Dry Years scenario.

#TODO discuss leads with tech team - harvest is playing a big role in the big dip - once you allow dry year in there you allow for harvest you only get a small dip and then rise again - Also increasing delta survival gets us above 500 spawners for a consecuative 5 year period everywhere… - The delta + outmigration survival gauntlet seems to be diminishing pops (all but tribs that are less strong get diminished ) - All of the default calibration tribs are starting out the simulation with very few spawners seeds show limited pops on all tribs except main ones

test_seeds <- fallRunDSM::adult_seeds
test_seeds[1] <- rowMeans(DSMCalibrationData::grandtab_imputed$fall)
# Dry Years --
new_params_dy <- fallRunDSM::r_to_r_dry_years_params
new_params_dy$movement_hypo_weights <- c(1, rep(0, 7))

# BASELINE --
new_params <- fallRunDSM::r_to_r_baseline_params
new_params$movement_hypo_weights <- c(1, rep(0, 7))

# seed
r2r_seeds_dy <- fallRunDSM::fall_run_model(mode = "seed",
                                           seeds = fallRunDSM::adult_seeds, 
                                        ..params =  new_params, # seed with baseline, then Dry Years
                                        delta_surv_inflation = FALSE)

# run model
r2r_model_results_dy <- fallRunDSM::fall_run_model(mode = "simulate",
                                                ..params =  new_params_dy,
                                                seeds = r2r_seeds_dy,
                                                delta_surv_inflation = TRUE)

Results

Model results should be evaluated relative to the Baseline model. The following plots show the % difference from baseline results for the Dry Years scenario. You can look at the tab to the right to see the total spawner trends of the Dry Years Scenario in comparison to the Baseline Scenario. (Make add a percent difference table in here too) - Think through the best way to present these. Also add a percent difference bar plot)

% Difference from Baseline (all watersheds)

% Difference from Baseline (all watersheds)

Spawners Plot

Diagnostic Plots

## Rows: 252
## Columns: 6
## $ month                  <chr> "jan", "jan", "jan", "jan", "jan", "jan", "jan"…
## $ year                   <chr> "1980", "1981", "1982", "1983", "1984", "1985",…
## $ flows                  <dbl> 767.0468, 523.8617, 438.7412, 854.6591, 340.708…
## $ date                   <date> 1980-01-01, 1981-01-01, 1982-01-01, 1983-01-01…
## $ sac_migratory_survival <dbl> 0.508, 0.508, 0.508, 0.508, 0.508, 0.508, 0.189…
## $ outmigration_month     <chr> "Outmigration Month", "Outmigration Month", "Ou…

## Rows: 682
## Columns: 4
## $ year                                    <chr> "1979", "1979", "1979", "1979"…
## $ location                                <chr> "American River", "Antelope Cr…
## $ average_monthly_annual_spawning_habitat <dbl> 960725.353, 60038.788, 1625.00…
## $ spawner_capacity                        <dbl> 103415, 6463, 175, 4700, 1646,…

## $fall
##                             1998   1999   2000   2001   2002   2003  2004  2005
## Upper Sacramento River      6318 161192  96688  75296  65690  89229 43604 57012
## Antelope Creek                72     72     72     72     72     72    72    72
## Battle Creek               53957  92929  53447 100604 397149  64764 23861 20520
## Bear Creek                    34     34     34     34     34     34    34    34
## Big Chico Creek               40     40     40     40     40     40    40    40
## Butte Creek                  500   1590   1590   4433   3665   3492  2516  4255
## Clear Creek                 4259   8003   6687  10865  16071   9475  6365 14824
## Cottonwood Creek            1355   1355   1355   1355   1355   1355  1355  1355
## Cow Creek                   1589   1589   1589   1589   1589   1589  1589  1589
## Deer Creek                   270    587    587    587    587    587   300   963
## Elder Creek                   40     40     40     40     40     40    40    40
## Mill Creek                   546   1218   1218   1218   2611   2426  1192  2426
## Paynes Creek                  85     85     85     85     85     85    85    85
## Stony Creek                   40     40     40     40     40     40    40    40
## Thomes Creek                  40     40     40     40     40     40    40    40
## Upper-mid Sacramento River     0      0      0      0      0      0     0     0
## Sutter Bypass                  0      0      0      0      0      0     0     0
## Bear River                    40     40     40     40     40     40    40    40
## Feather River              58742  58742 106490 165833  97621  83495 50286 45634
## Yuba River                 28860  22492  13920  21714  22326  26285  4837  9106
## Lower-mid Sacramento River     0      0      0      0      0      0     0     0
## Yolo Bypass                    0      0      0      0      0      0     0     0
## American River             50457  55339 100852 135384 124252 163742 99230 62679
## Lower Sacramento River         0      0      0      0      0      0     0     0
## Calaveras River               40     40     40     40     40     40    40    40
## Cosumnes River               300    229    460    531   1350    122  1208   370
## Mokelumne River             4122   2183   1973   2307   2840   2122  1588 10406
## Merced River                3292   3129  11130   9181   8866   2530  3270  1942
## Stanislaus River            3087   4349   8498   7033   7787   5902  4015  1427
## Tuolumne River              8910   8232  17873   8782   7173   2163  1984   668
## San Joaquin River              0      0      0      0      0      0     0     0
##                             2006  2007  2008 2009  2010  2011  2012   2013
## Upper Sacramento River     55468 17061 24743 5827 16372 11957 28701  40084
## Antelope Creek                72    72    72   72    72    72    72     72
## Battle Creek               19493  9904  4286 3047  6632 12513 31554  30834
## Bear Creek                    34   140    19    6    34    34    34     34
## Big Chico Creek               40    40    40   40    40    40    40     40
## Butte Creek                 1920  1225   275  306   370   416   813   2200
## Clear Creek                 8422  4157  7677 3228  7192  4841  7631  13337
## Cottonwood Creek            1355  1250   510 1055  1137  2144  2556   2774
## Cow Creek                   4209  2044   478  261   536  1810  1488   3011
## Deer Creek                  1905   563   194   58   166   662   873   1026
## Elder Creek                   40    40    40   40    40    40    40     40
## Mill Creek                  1403   851   218  102   144  1231   890   2197
## Paynes Creek                  85    85    85   85    85    85    85    175
## Stony Creek                   40    40    40   40    40    40    40     40
## Thomes Creek                  40    40    40   40    40    40    40     40
## Upper-mid Sacramento River     0     0     0    0     0     0     0      0
## Sutter Bypass                  0     0     0    0     0     0     0      0
## Bear River                    40    40    40   40    40    40    40     40
## Feather River              70934 20338  5513 4499 41693 43898 59084 140365
## Yuba River                  4029  1007  1236 2770  4163  6794  5450  11181
## Lower-mid Sacramento River     0     0     0    0     0     0     0      0
## Yolo Bypass                    0     0     0    0     0     0     0      0
## American River             24540 10120  2514 5297 14688 25626 38328  58228
## Lower Sacramento River         0     0     0    0     0     0     0      0
## Calaveras River               40    40    40   40    40    40    40     40
## Cosumnes River               530    77    15  531   740    53  1071    531
## Mokelumne River             1732   470   173  680  1920  2674  5471   7071
## Merced River                1429   485   389  358   651  1571  2011   2826
## Stanislaus River            1923   443   865  595  1086  1309  4006   2845
## Tuolumne River               562   224   388  124   540   893   783   1926
## San Joaquin River              0     0     0    0     0     0     0      0
##                             2014  2015  2016 2017
## Upper Sacramento River     34876 28660  4291 2149
## Antelope Creek               143     6   138    3
## Battle Creek               27064  3642  1236  354
## Bear Creek                    34     2    32    2
## Big Chico Creek               40    40    40   40
## Butte Creek                 1412    82   626  105
## Clear Creek                15794  8809  2481 2353
## Cottonwood Creek            1940   604   813  124
## Cow Creek                   3535   591   822  288
## Deer Creek                   849   612   253  106
## Elder Creek                   40    40    40   40
## Mill Creek                  2488  1033   602  342
## Paynes Creek                  72    85     8   85
## Stony Creek                   40    40    40   40
## Thomes Creek                  40    40    40   40
## Upper-mid Sacramento River     0     0     0    0
## Sutter Bypass                  0     0     0    0
## Bear River                    40    40    40   40
## Feather River              56811 19091 35994 9779
## Yuba River                  9757  6567  3766 1517
## Lower-mid Sacramento River     0     0     0    0
## Yolo Bypass                    0     0     0    0
## American River             26475 15732 14473 9886
## Lower Sacramento River         0     0     0    0
## Calaveras River               40    40    40   40
## Cosumnes River               373   204  1248  670
## Mokelumne River             3297  4581  1984 5639
## Merced River                 922  1247  2541 3191
## Stanislaus River            3060  6136  9330 5655
## Tuolumne River               438   113  1347 1096
## San Joaquin River              0     0     0    0
## 
## $late_fall
##                             1998 1999 2000  2001  2002 2003 2004  2005  2006
## Upper Sacramento River     39340 8683 8702 19276 36004 5494 8824 10524 10163
## Antelope Creek                 0    0    0     0     0    0    0     0     0
## Battle Creek                  61   61   61    98   216   57   40    23    50
## Bear Creek                     0    0    0     0     0    0    0     0     0
## Big Chico Creek                0    0    0     0     0    0    0     0     0
## Butte Creek                    0    0    0     0     0    0    0     0     0
## Clear Creek                  100  100  100   100   100  110   60    94    42
## Cottonwood Creek               0    0    0     0     0    0    0     0     0
## Cow Creek                      0    0    0     0     0    0    0     0     0
## Deer Creek                     0    0    0     0     0    0    0     0     0
## Elder Creek                    0    0    0     0     0    0    0     0     0
## Mill Creek                     0    0    0     0     0    0    0     0     0
## Paynes Creek                   0    0    0     0     0    0    0     0     0
## Stony Creek                    0    0    0     0     0    0    0     0     0
## Thomes Creek                   0    0    0     0     0    0    0     0     0
## Upper-mid Sacramento River     0    0    0     0     0    0    0     0     0
## Sutter Bypass                  0    0    0     0     0    0    0     0     0
## Bear River                     0    0    0     0     0    0    0     0     0
## Feather River                  0    0    0     0     0    0    0     0     0
## Yuba River                     0    0    0     0     0    0    0     0     0
## Lower-mid Sacramento River     0    0    0     0     0    0    0     0     0
## Yolo Bypass                    0    0    0     0     0    0    0     0     0
## American River                 0    0    0     0     0    0    0     0     0
## Lower Sacramento River         0    0    0     0     0    0    0     0     0
## Calaveras River                0    0    0     0     0    0    0     0     0
## Cosumnes River                 0    0    0     0     0    0    0     0     0
## Mokelumne River                0    0    0     0     0    0    0     0     0
## Merced River                   0    0    0     0     0    0    0     0     0
## Stanislaus River               0    0    0     0     0    0    0     0     0
## Tuolumne River                 0    0    0     0     0    0    0     0     0
## San Joaquin River              0    0    0     0     0    0    0     0     0
##                             2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
## Upper Sacramento River     15275 3964 3334 4282 3686 2822 5227 7950 2131 3085
## Antelope Creek                 0    0    0    0    0    0    0    0    0    0
## Battle Creek                  72   19   32   27   28   19   42  120   97   57
## Bear Creek                     0    0    0    0    0    0    0    0    0    0
## Big Chico Creek                0    0    0    0    0    0    0    0    0    0
## Butte Creek                    0    0    0    0    0    0    0    0    0    0
## Clear Creek                   69   55  336   91   58   50   77   72  272   55
## Cottonwood Creek               0    0    0    0    0    0    0    0    0    0
## Cow Creek                      0    0    0    0    0    0    0    0    0    0
## Deer Creek                     0    0    0    0    0    0    0    0    0    0
## Elder Creek                    0    0    0    0    0    0    0    0    0    0
## Mill Creek                     0    0    0    0    0    0    0    0    0    0
## Paynes Creek                   0    0    0    0    0    0    0    0    0    0
## Stony Creek                    0    0    0    0    0    0    0    0    0    0
## Thomes Creek                   0    0    0    0    0    0    0    0    0    0
## Upper-mid Sacramento River     0    0    0    0    0    0    0    0    0    0
## Sutter Bypass                  0    0    0    0    0    0    0    0    0    0
## Bear River                     0    0    0    0    0    0    0    0    0    0
## Feather River                  0    0    0    0    0    0    0    0    0    0
## Yuba River                     0    0    0    0    0    0    0    0    0    0
## Lower-mid Sacramento River     0    0    0    0    0    0    0    0    0    0
## Yolo Bypass                    0    0    0    0    0    0    0    0    0    0
## American River                 0    0    0    0    0    0    0    0    0    0
## Lower Sacramento River         0    0    0    0    0    0    0    0    0    0
## Calaveras River                0    0    0    0    0    0    0    0    0    0
## Cosumnes River                 0    0    0    0    0    0    0    0    0    0
## Mokelumne River                0    0    0    0    0    0    0    0    0    0
## Merced River                   0    0    0    0    0    0    0    0    0    0
## Stanislaus River               0    0    0    0    0    0    0    0    0    0
## Tuolumne River                 0    0    0    0    0    0    0    0    0    0
## San Joaquin River              0    0    0    0    0    0    0    0    0    0
##                            2017
## Upper Sacramento River     3069
## Antelope Creek                0
## Battle Creek                 43
## Bear Creek                    0
## Big Chico Creek               0
## Butte Creek                   0
## Clear Creek                  55
## Cottonwood Creek              0
## Cow Creek                     0
## Deer Creek                    0
## Elder Creek                   0
## Mill Creek                    0
## Paynes Creek                  0
## Stony Creek                   0
## Thomes Creek                  0
## Upper-mid Sacramento River    0
## Sutter Bypass                 0
## Bear River                    0
## Feather River                 0
## Yuba River                    0
## Lower-mid Sacramento River    0
## Yolo Bypass                   0
## American River                0
## Lower Sacramento River        0
## Calaveras River               0
## Cosumnes River                0
## Mokelumne River               0
## Merced River                  0
## Stanislaus River              0
## Tuolumne River                0
## San Joaquin River             0
## 
## $winter
##                            1998 1999 2000 2001 2002 2003 2004  2005  2006 2007
## Upper Sacramento River     2893 3264 1261 8120 7337 8133 7784 15730 17197 2487
## Antelope Creek                0    0    0    0    0    0    0     0     0    0
## Battle Creek                347  391  151  973  879  975  933  1885  2061  298
## Bear Creek                    0    0    0    0    0    0    0     0     0    0
## Big Chico Creek               0    0    0    0    0    0    0     0     0    0
## Butte Creek                   0    0    0    0    0    0    0     0     0    0
## Clear Creek                   0    0    0    0    0    0    0     0     0    0
## Cottonwood Creek              0    0    0    0    0    0    0     0     0    0
## Cow Creek                     0    0    0    0    0    0    0     0     0    0
## Deer Creek                    0    0    0    0    0    0    0     0     0    0
## Elder Creek                   0    0    0    0    0    0    0     0     0    0
## Mill Creek                    0    0    0    0    0    0    0     0     0    0
## Paynes Creek                  0    0    0    0    0    0    0     0     0    0
## Stony Creek                   0    0    0    0    0    0    0     0     0    0
## Thomes Creek                  0    0    0    0    0    0    0     0     0    0
## Upper-mid Sacramento River    0    0    0    0    0    0    0     0     0    0
## Sutter Bypass                 0    0    0    0    0    0    0     0     0    0
## Bear River                    0    0    0    0    0    0    0     0     0    0
## Feather River                 0    0    0    0    0    0    0     0     0    0
## Yuba River                    0    0    0    0    0    0    0     0     0    0
## Lower-mid Sacramento River    0    0    0    0    0    0    0     0     0    0
## Yolo Bypass                   0    0    0    0    0    0    0     0     0    0
## American River                0    0    0    0    0    0    0     0     0    0
## Lower Sacramento River        0    0    0    0    0    0    0     0     0    0
## Calaveras River               0    0    0    0    0    0    0     0     0    0
## Cosumnes River                0    0    0    0    0    0    0     0     0    0
## Mokelumne River               0    0    0    0    0    0    0     0     0    0
## Merced River                  0    0    0    0    0    0    0     0     0    0
## Stanislaus River              0    0    0    0    0    0    0     0     0    0
## Tuolumne River                0    0    0    0    0    0    0     0     0    0
## San Joaquin River             0    0    0    0    0    0    0     0     0    0
##                            2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
## Upper Sacramento River     2725 4416 1533  738 2578 5920 2627 3182 1409  795
## Antelope Creek                0    0    0    0    0    0    0    0    0    0
## Battle Creek                327  529  184   88  309  709  315  381  169   95
## Bear Creek                    0    0    0    0    0    0    0    0    0    0
## Big Chico Creek               0    0    0    0    0    0    0    0    0    0
## Butte Creek                   0    0    0    0    0    0    0    0    0    0
## Clear Creek                   0    0    0    0    0    0    0    0    0    0
## Cottonwood Creek              0    0    0    0    0    0    0    0    0    0
## Cow Creek                     0    0    0    0    0    0    0    0    0    0
## Deer Creek                    0    0    0    0    0    0    0    0    0    0
## Elder Creek                   0    0    0    0    0    0    0    0    0    0
## Mill Creek                    0    0    0    0    0    0    0    0    0    0
## Paynes Creek                  0    0    0    0    0    0    0    0    0    0
## Stony Creek                   0    0    0    0    0    0    0    0    0    0
## Thomes Creek                  0    0    0    0    0    0    0    0    0    0
## Upper-mid Sacramento River    0    0    0    0    0    0    0    0    0    0
## Sutter Bypass                 0    0    0    0    0    0    0    0    0    0
## Bear River                    0    0    0    0    0    0    0    0    0    0
## Feather River                 0    0    0    0    0    0    0    0    0    0
## Yuba River                    0    0    0    0    0    0    0    0    0    0
## Lower-mid Sacramento River    0    0    0    0    0    0    0    0    0    0
## Yolo Bypass                   0    0    0    0    0    0    0    0    0    0
## American River                0    0    0    0    0    0    0    0    0    0
## Lower Sacramento River        0    0    0    0    0    0    0    0    0    0
## Calaveras River               0    0    0    0    0    0    0    0    0    0
## Cosumnes River                0    0    0    0    0    0    0    0    0    0
## Mokelumne River               0    0    0    0    0    0    0    0    0    0
## Merced River                  0    0    0    0    0    0    0    0    0    0
## Stanislaus River              0    0    0    0    0    0    0    0    0    0
## Tuolumne River                0    0    0    0    0    0    0    0    0    0
## San Joaquin River             0    0    0    0    0    0    0    0    0    0
## 
## $spring
##                             1998 1999 2000  2001  2002  2003  2004  2005 2006
## Upper Sacramento River      1115  262   43   621   195   326   370    30  326
## Antelope Creek               154   40    9     8    46    46     3    82  102
## Battle Creek                 178   73   78   111   222   221    90    73  221
## Bear Creek                     0    0    0     0     0     0     0     0    0
## Big Chico Creek              369   27   27    39   101    81   101    37  299
## Butte Creek                20259 3679 4118 18670 16409 17404 10558 17592 6537
## Clear Creek                   47   35    9    99    66    25    98    69   77
## Cottonwood Creek             477  102  122   245   125    73    17    47   55
## Cow Creek                      0    0    0     0     0     0     0     0    0
## Deer Creek                  1879 1591  637  1622  2195  2759   804  2239 2432
## Elder Creek                    0    0    0     0     0     0     0     0    0
## Mill Creek                   424  560  544  1104  1594  1426   998  1150 1002
## Paynes Creek                   0    0    0     0     0     0     0     0    0
## Stony Creek                    0    0    0     0     0     0     0     0    0
## Thomes Creek                   1    2    2     2     2     2     2     2    2
## Upper-mid Sacramento River     0    0    0     0     0     0     0     0    0
## Sutter Bypass                  0    0    0     0     0     0     0     0    0
## Bear River                     0    0    0     0     0     0     0     0    0
## Feather River               4538 4538 8227 12812  7542  6451  3885  3526 5480
## Yuba River                  2230 1738 1075  1678  1725  2031  1618  5274 1456
## Lower-mid Sacramento River     0    0    0     0     0     0     0     0    0
## Yolo Bypass                    0    0    0     0     0     0     0     0    0
## American River                 0    0    0     0     0     0     0     0    0
## Lower Sacramento River         0    0    0     0     0     0     0     0    0
## Calaveras River               40   40   40    40    40    40    40    40   40
## Cosumnes River                40   40   40    40    40    40    40    40   40
## Mokelumne River               40   40   40    40    40    40    40    40   40
## Merced River                  40   40   40    40    40    40    40    40   40
## Stanislaus River              40   40   40    40    40    40    40    40   40
## Tuolumne River                40   40   40    40    40    40    40    40   40
## San Joaquin River              0    0    0     0     0     0     0     0    0
##                            2007  2008 2009 2010 2011  2012  2013 2014 2015 2016
## Upper Sacramento River      248    52  326  326  326   326   326  326  326  326
## Antelope Creek               26     3   32   17    6     1    32    7    5    7
## Battle Creek                291   105  194  172  157   799   608  429  181  180
## Bear Creek                    0     0    0    0    0     0     0    0    0    0
## Big Chico Creek             101   101    6    2  124   101   101  101  101  101
## Butte Creek                6871 11046 2687 1991 4871 16317 16782 5083  569 5731
## Clear Creek                 194   200  120   21    8    68   659   95   45   29
## Cottonwood Creek             34    88   88   15    2     1     1    2   88   88
## Cow Creek                     0     0    0    0    0     0     0    0    0    0
## Deer Creek                  644   140  213  262  271   734   708  830  268  331
## Elder Creek                   0     0    0    0    0     0     0    0    0    0
## Mill Creek                  920   381  220  482  366   768   644  679  127  175
## Paynes Creek                  0     0    0    0    0     0     0    0    0    0
## Stony Creek                   0     0    0    0    0     0     0    0    0    0
## Thomes Creek                  2     2    2    2    2     2     2    2    2    2
## Upper-mid Sacramento River    0     0    0    0    0     0     0    0    0    0
## Sutter Bypass                 0     0    0    0    0     0     0    0    0    0
## Bear River                    0     0    0    0    0     0     0    0    0    0
## Feather River              1571   426  348 3221 3391  4565 10844 4389 1475 2781
## Yuba River                  353  1320 2616 3737 2360  2289  4046 2021  235  291
## Lower-mid Sacramento River    0     0    0    0    0     0     0    0    0    0
## Yolo Bypass                   0     0    0    0    0     0     0    0    0    0
## American River                0     0    0    0    0     0     0    0    0    0
## Lower Sacramento River        0     0    0    0    0     0     0    0    0    0
## Calaveras River              40    40   40   40   40    40    40   40   40   40
## Cosumnes River               40    40   40   40   40    40    40   40   40   40
## Mokelumne River              40    40   40   40   40    40    40   40   40   40
## Merced River                 40    40   40   40   40    40    40   40   40   40
## Stanislaus River             40    40   40   40   40    40    40   40   40   40
## Tuolumne River               40    40   40   40   40    40    40   40   40   40
## San Joaquin River             0     0    0    0    0     0     0    0    0    0
##                            2017
## Upper Sacramento River      326
## Antelope Creek                8
## Battle Creek                 30
## Bear Creek                    0
## Big Chico Creek             101
## Butte Creek                 565
## Clear Creek                  25
## Cottonwood Creek             88
## Cow Creek                     0
## Deer Creek                  219
## Elder Creek                   0
## Mill Creek                  258
## Paynes Creek                  0
## Stony Creek                   0
## Thomes Creek                  2
## Upper-mid Sacramento River    0
## Sutter Bypass                 0
## Bear River                    0
## Feather River               756
## Yuba River                  117
## Lower-mid Sacramento River    0
## Yolo Bypass                   0
## American River                0
## Lower Sacramento River        0
## Calaveras River              40
## Cosumnes River               40
## Mokelumne River              40
## Merced River                 40
## Stanislaus River             40
## Tuolumne River               40
## San Joaquin River             0

Threshold Biological Performance Metrics

The two tabs below show plots that describe if a tributary meets the recovery objective.

(TODO: maybe color indicator pops differently)

Abundance and Genetic Diversity

Productivity Metrics

Additional Biological Performance Metics

Spatial Structure

## Rows: 1,240
## Columns: 12
## $ location                  <chr> "American River", "American River", "America…
## $ year                      <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1…
## $ scenario                  <chr> "Dry Years", "Dry Years", "Dry Years", "Dry …
## $ run                       <chr> "fall", "fall", "fall", "fall", "fall", "fal…
## $ performance_metric        <chr> "1 All Spawners", "1 All Spawners", "1 All S…
## $ value                     <dbl> 105670, 61527, 115575, 203233, 123711, 14130…
## $ origin                    <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ size_or_age               <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ month                     <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ `Spawners Present`        <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
## $ diversity_group           <fct> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,…
## $ div_group_with_watersheds <chr> "5:", "5:", "5:", "5:", "5:", "5:", "5:", "5…
## # A tibble: 4 × 1
##   location              
##   <chr>                 
## 1 Battle Creek          
## 2 Bear Creek            
## 3 Cow Creek             
## 4 Upper Sacramento River

Life History Diversity